A critical aspect in the modeling of biological systems is the description view point. On the one hand, the Stochastic π-calculus formalism provides an intuitive and compact representation from an internal perspective. On the other hand, other proposed languages such as Hybrid Automata and Stochastic Concurrent Constraint Programming introduce in the system description an external control and provide more structured models. This work aims at bridging the above discussed gap. In particular, we propose a different approach for the encoding of biological systems in Stochastic π-calculus in the direction of introducing an external control and comparing different formalisms. We show the effectiveness of our method on some examples.